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A comprehensive analysis of gorilla-specific LINE-1 retrotransposons

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Abstract

Background

Long interspersed element-1 (LINE-1 or L1) is the most abundant retrotransposons in the primate genome. They have approximately 520,000 copies and make up ~ 17% of the primate genome. Full-length L1s can mobilize to a new genomic location using their enzymatic machinery. Gorilla is the second closest species to humans after the chimpanzee, and human-gorilla split 7–12 million years ago. The gorilla genome provides an opportunity to explore primate origins and evolution.

Objective

L1s have contributed to genome diversity and variations during primate evolution. This study aimed to identify gorilla-specific L1s using a more recent version of the gorilla reference genome (Mar. 2016 GSMRT3/gorGor5).

Methods

We collected gorilla-specific L1 candidates through computational analysis and manual inspection. L1Xplorer was used to identify whether full-length gorilla-specific L1s were intact. In addition, to determine the level of sequence conservation between intact fulllength gorilla-specific L1s, two ORFs of intact L1s were aligned with the L1PA2 consensus sequence.

Results

2002 gorilla-specific L1 candidates were identified through computational analysis. Among them, we manually inspected 1,883 gorilla-specific L1s, among which most of them belong to the L1PA2 subfamily and 12 were intact L1s that could influence genomic variations in the gorilla genome. Interestingly, the 12 intact full-length gorilla-specific L1s have 14 highly conserved nonsynonymous mutations, including 6 mutations and 8 mutations in ORF1 and ORF2, respectively. In comparison to the intact full-length chimpanzee-specific L1s and human-specific hot-L1s, two of these in ORF1 (L256F and E293G) were shown as gorilla-specific nonsynonymous mutations.

Conclusion

The gorilla-specific L1s may have had significantly affected the gorilla genome to compose a genome different form that of other primates during primate evolution.

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Acknowledgements

This research was enabled in part by support provided by SHARCNET (www.sharcnet.ca) and Compute Canada (www.computecanada.ca). This research was supported by funding from Basic Science Research Capacity Enhancement Project through Korea Basic Science Institute (National research Facilities and Equipment Center) Grant by the Ministry of Education (Grant No. 2019R1A6C1010033) to K.H. and NSERC Discovery Grant (RGPIN-2017-06785) to P.L. The Department of Microbiology was supported through the Research-Focused Department Promotion Project as a part of the University Innovation Support Program for Dankook University in 2021.

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Authors and Affiliations

  1. Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea

    Soyeon Jeon, Songmi Kim, Man Hwan Oh & Kyudong Han

  2. Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea

    Songmi Kim & Kyudong Han

  3. Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada

    Ping Liang & Wanxiangfu Tang

  4. Centre of Biotechnologies, Brock University, St. Catharines, ON, L2S 3A1, Canada

    Ping Liang

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  1. Soyeon Jeon
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Supplementary Information

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13258_2021_1146_MOESM1_ESM.pdf

Supplementary Fig. S1 Examples of removed gorilla L1 candidates. In UCSC Genome Browser, two copies of TE (red and blue boxes) were detected. However, through manual inspection, two copies of TEs were identified as one copy of TE (PDF 80 KB)

13258_2021_1146_MOESM2_ESM.pdf

Supplementary Fig. S2 Chromosomal distribution of 1,858 gorilla-specific L1s. The dark blue bars indicate the density (number of L1s/Mbp) of gorilla-specific L1s in each chromosome. The hatching blue boxes denote the density of full-length L1s. The density of unknown chromosome (25 loci) were not included (PDF 31 KB)

13258_2021_1146_MOESM3_ESM.pdf

Supplementary Fig. S3 Alignment of 12 intact full-length gorilla-specific L1s, 9 intact full-length chimpanzee-specific L1s, and 90 human hot-L1s with L1PA consensus sequences (ORF1). By using BioEdit program, ORF1 region of gorilla, chimpanzee, human L1s were aligned with four L1PA consensus sequences (L1PA2, L1PA3, L1PA4, and L1PA5). Yellow, blue, and green boxes denote gorilla, chimpanzee, and human L1s, respectively. Red boxes indicate missense mutations of 12 gorilla-specific intact L1s (PDF 1867 KB)

13258_2021_1146_MOESM4_ESM.pdf

Supplementary Fig. S4 Alignment of 12 intact full-length gorilla-specific L1s, 9 intact full-length chimpanzee-specific L1s, and 90 human hot-L1s with L1PA consensus sequences (ORF2). By using BioEdit program, ORF2 region of gorilla, chimpanzee, human L1s were aligned with four L1PA consensus sequences (L1PA2, L1PA3, L1PA4, and L1PA5). Yellow, blue, and green boxes denote gorilla, chimpanzee, and human L1s, respectively. Red boxes indicate missense mutations of 12 gorilla-specific intact L1s (PDF 7393 KB)

Supplementary Table S1 The 1,883 L1 elements in the gorilla genome (XLSX 114 KB)

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Jeon, S., Kim, S., Oh, M.H. et al. A comprehensive analysis of gorilla-specific LINE-1 retrotransposons. Genes Genom 43, 1133–1141 (2021). https://doi.org/10.1007/s13258-021-01146-4

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